# module load samtools
# module load picard/2.8.2
# module load bwa/0.7.17
# module load java fgbio
# ========= [INFO] ==========
# Path In : /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output
# Type In : .unmapped.bam
# MS Info : /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/tabMSInfo.9MS.txt
# minReadByGrp: 3
# Rep Fusion : /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/
# Rep Profil : /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/4_MSprofil_min3ReadByGrp/
# List fusion: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3-5_BAM_Fusion_min3ReadByGrp.log
# minLen : 
# =============================
#

# ====== [ I. 1. Creat .LIBRARY_PARAMS.txt ] =====
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/220204_NS500487_0027_AHFCJLAFX3_min3ReadByGrp.LIBRARY_PARAMS.txt ]

# ====== [ 2. Fusion file ] =====
#File_Name_Fusion	nb_found[4]
10-N3-12cycles-IDT.unmapped.bam	4
7-N3-12cycles-IDT.unmapped.bam	4
8-N3-12cycles-IDT.unmapped.bam	4
9-N3-12cycles-IDT.unmapped.bam	4
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//10-N3-12cycles-IDT.unmapped.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//7-N3-12cycles-IDT.unmapped.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//8-N3-12cycles-IDT.unmapped.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//9-N3-12cycles-IDT.unmapped.bam ]
# ====== [ 3. Mapp Reads/BWA ] ====== 
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.unmapped.bam CATGTAGTC TCTCT A A15
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A15.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A15.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.merged.withUMI.bam ]
#-------

# Thu Jun 27 14:36:07 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.unmapped.bam GTGATAGTC TCTCT A A20
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A20.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A20.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.merged.withUMI.bam ]
#-------

# Thu Jun 27 14:53:56 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.unmapped.bam GACTTAGTC TCTCT A A25
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A25.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A25.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.merged.withUMI.bam ]
#-------

# Thu Jun 27 15:11:33 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.unmapped.bam GTATGTG TATGG AC AC15
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC15.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC15.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.merged.withUMI.bam ]
#-------

# Thu Jun 27 15:20:22 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.unmapped.bam CTCGGTG TATGG AC AC20
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC20.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC20.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.merged.withUMI.bam ]
#-------

# Thu Jun 27 15:28:49 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.unmapped.bam ACAGGTG TATGG AC AC25
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC25.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC25.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.merged.withUMI.bam ]
#-------

# Thu Jun 27 15:37:15 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.unmapped.bam AGTCGTG CGTGG AT AT15
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT15.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT15.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.merged.withUMI.bam ]
#-------

# Thu Jun 27 15:46:03 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.unmapped.bam TCAGGTG CGTGG AT AT20
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT20.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT20.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.merged.withUMI.bam ]
#-------

# Thu Jun 27 15:54:51 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.unmapped.bam GTCAGTG CGTGG AT AT25
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT25.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT25.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:03:26 CEST 2024
# Thu Jun 27 16:03:26 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.unmapped.bam CATGTAGTC TCTCT A A15
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A15.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A15.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:07:12 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.unmapped.bam GTGATAGTC TCTCT A A20
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A20.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A20.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:10:57 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.unmapped.bam GACTTAGTC TCTCT A A25
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A25.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A25.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:14:42 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.unmapped.bam GTATGTG TATGG AC AC15
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC15.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC15.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:16:41 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.unmapped.bam CTCGGTG TATGG AC AC20
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC20.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC20.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:18:35 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.unmapped.bam ACAGGTG TATGG AC AC25
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC25.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC25.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:20:28 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.unmapped.bam AGTCGTG CGTGG AT AT15
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT15.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT15.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:22:22 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.unmapped.bam TCAGGTG CGTGG AT AT20
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT20.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT20.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:24:16 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.unmapped.bam GTCAGTG CGTGG AT AT25
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT25.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT25.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:26:07 CEST 2024
# Thu Jun 27 16:26:07 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.unmapped.bam CATGTAGTC TCTCT A A15
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A15.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A15.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:27:44 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.unmapped.bam GTGATAGTC TCTCT A A20
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A20.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A20.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:29:19 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.unmapped.bam GACTTAGTC TCTCT A A25
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A25.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A25.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:30:54 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.unmapped.bam GTATGTG TATGG AC AC15
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC15.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC15.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:31:44 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.unmapped.bam CTCGGTG TATGG AC AC20
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC20.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC20.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:32:31 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.unmapped.bam ACAGGTG TATGG AC AC25
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC25.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC25.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:33:19 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.unmapped.bam AGTCGTG CGTGG AT AT15
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT15.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT15.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:34:11 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.unmapped.bam TCAGGTG CGTGG AT AT20
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT20.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT20.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:35:02 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.unmapped.bam GTCAGTG CGTGG AT AT25
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT25.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT25.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:35:53 CEST 2024
# Thu Jun 27 16:35:53 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.unmapped.bam CATGTAGTC TCTCT A A15
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A15.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A15.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:40:37 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.unmapped.bam GTGATAGTC TCTCT A A20
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A20.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A20.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:45:21 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.unmapped.bam GACTTAGTC TCTCT A A25
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A25.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_A25.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:50:03 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.unmapped.bam GTATGTG TATGG AC AC15
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC15.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC15.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:52:16 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.unmapped.bam CTCGGTG TATGG AC AC20
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC20.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC20.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:54:27 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.unmapped.bam ACAGGTG TATGG AC AC25
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC25.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AC25.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:56:35 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.unmapped.bam AGTCGTG CGTGG AT AT15
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT15.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT15.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.merged.withUMI.bam ]
#-------

# Thu Jun 27 16:58:55 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.unmapped.bam TCAGGTG CGTGG AT AT20
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT20.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT20.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.merged.withUMI.bam ]
#-------

# Thu Jun 27 17:01:14 CEST 2024
# > pipe_UMI_IDT_MS_SimulRefVersion_etap1_unSelectBam2Bam.sh /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.unmapped.bam GTCAGTG CGTGG AT AT25
# > java -jar /env/gfs/apps/picard/2.8.2/picard.jar SamToFastq I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.unmapped.bam F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 8  /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT25.fa /dev/stdin | java -jar /env/gfs/apps/picard/2.8.2/picard.jar MergeBamAlignment UNMAPPED=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.unmapped.bam ALIGNED=/dev/stdin O= R=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier//Ref/RefMSSeq//refMS_AT25.fa SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.merged.withUMI.bam ]
#-------

# Thu Jun 27 17:03:28 CEST 2024
# Thu Jun 27 17:03:28 CEST 2024
# ====== [ II. Call Consensus Reads ] === < 1.Group Reads By Umi >
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 17:13:00 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 17:15:23 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 17:17:39 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 17:28:12 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 17:33:40 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 17:35:36 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 17:46:33 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 17:55:59 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:02:26 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:02:49 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:03:05 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:03:23 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:03:46 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:04:06 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:04:22 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:04:45 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:05:06 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:05:24 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:05:43 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:05:57 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:06:12 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:06:31 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:06:48 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:07:02 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:07:20 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:07:38 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:07:56 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:09:27 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:09:56 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:10:25 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:11:54 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:12:42 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:13:01 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:14:32 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:15:51 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam ]
 -------

# Thu Jun 27 18:16:48 CEST 2024
# ====== [ Call Consensus Reads ] === < 2. Call Molecular Consensus Reads >
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# Thu Jun 27 18:29:06 CEST 2024
# ====== [ Call Consensus Reads ] === < 3. profils analysis >
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq CATGTAGTC TCTCT A A15
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq CATGTAGTC TCTCT A A15
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTGATAGTC TCTCT A A20
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTGATAGTC TCTCT A A20
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GACTTAGTC TCTCT A A25
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GACTTAGTC TCTCT A A25
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTATGTG TATGG AC AC15
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTATGTG TATGG AC AC15
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq CTCGGTG TATGG AC AC20
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq CTCGGTG TATGG AC AC20
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ACAGGTG TATGG AC AC25
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ACAGGTG TATGG AC AC25
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq AGTCGTG CGTGG AT AT15
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq AGTCGTG CGTGG AT AT15
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq TCAGGTG CGTGG AT AT20
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq TCAGGTG CGTGG AT AT20
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTCAGTG CGTGG AT AT25
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTCAGTG CGTGG AT AT25
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq CATGTAGTC TCTCT A A15
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq CATGTAGTC TCTCT A A15
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTGATAGTC TCTCT A A20
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTGATAGTC TCTCT A A20
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GACTTAGTC TCTCT A A25
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GACTTAGTC TCTCT A A25
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTATGTG TATGG AC AC15
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTATGTG TATGG AC AC15
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq CTCGGTG TATGG AC AC20
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq CTCGGTG TATGG AC AC20
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ACAGGTG TATGG AC AC25
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ACAGGTG TATGG AC AC25
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq AGTCGTG CGTGG AT AT15
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq AGTCGTG CGTGG AT AT15
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq TCAGGTG CGTGG AT AT20
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq TCAGGTG CGTGG AT AT20
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTCAGTG CGTGG AT AT25
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTCAGTG CGTGG AT AT25
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq CATGTAGTC TCTCT A A15
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq CATGTAGTC TCTCT A A15
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTGATAGTC TCTCT A A20
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTGATAGTC TCTCT A A20
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GACTTAGTC TCTCT A A25
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GACTTAGTC TCTCT A A25
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTATGTG TATGG AC AC15
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTATGTG TATGG AC AC15
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq CTCGGTG TATGG AC AC20
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq CTCGGTG TATGG AC AC20
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ACAGGTG TATGG AC AC25
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ACAGGTG TATGG AC AC25
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq AGTCGTG CGTGG AT AT15
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq AGTCGTG CGTGG AT AT15
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq TCAGGTG CGTGG AT AT20
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq TCAGGTG CGTGG AT AT20
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTCAGTG CGTGG AT AT25
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTCAGTG CGTGG AT AT25
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq CATGTAGTC TCTCT A A15
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq CATGTAGTC TCTCT A A15
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTGATAGTC TCTCT A A20
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTGATAGTC TCTCT A A20
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GACTTAGTC TCTCT A A25
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GACTTAGTC TCTCT A A25
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTATGTG TATGG AC AC15
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTATGTG TATGG AC AC15
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq CTCGGTG TATGG AC AC20
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq CTCGGTG TATGG AC AC20
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ACAGGTG TATGG AC AC25
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ACAGGTG TATGG AC AC25
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq AGTCGTG CGTGG AT AT15
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq AGTCGTG CGTGG AT AT15
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq TCAGGTG CGTGG AT AT20
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq TCAGGTG CGTGG AT AT20
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTCAGTG CGTGG AT AT25
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTCAGTG CGTGG AT AT25
# ========[ END ]========
# Thu Jun 27 18:34:14 CEST 2024
# module load samtools
# module load picard/2.8.2
# module load bwa/0.7.17
# module load java fgbio
# ========= [INFO] ==========
# Path In : /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output
# Type In : .unmapped.bam
# MS Info : /env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Ref/tabMSInfo.9MS.txt
# minReadByGrp: 3
# Rep Fusion : /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/
# Rep Profil : /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/4_MSprofil_min3ReadByGrp/
# List fusion: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3-5_BAM_Fusion_min3ReadByGrp.log
# minLen : 
# =============================
#

# ====== [ I. 1. Creat .LIBRARY_PARAMS.txt ] =====
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/220204_NS500487_0027_AHFCJLAFX3_min3ReadByGrp.LIBRARY_PARAMS.txt ]

# ====== [ 2. Fusion file ] =====
#File_Name_Fusion	nb_found[4]
10-N3-12cycles-IDT.unmapped.bam	4
7-N3-12cycles-IDT.unmapped.bam	4
8-N3-12cycles-IDT.unmapped.bam	4
9-N3-12cycles-IDT.unmapped.bam	4
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//> ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//MS_profile_analysis_inputSeqVersion.sh ]
# module load samtools
# module load picard/2.8.2
# module load bwa/0.7.17
# module load java fgbio
# ========= [INFO] ==========
# Path In : /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output
# Type In : .unmapped.bam
# MS Info : /env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Ref/tabMSInfo.9MS.txt
# minReadByGrp: 3
# Rep Fusion : /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/
# Rep Profil : /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/4_MSprofil_min3ReadByGrp/
# List fusion: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3-5_BAM_Fusion_min3ReadByGrp.log
# minLen : 
# =============================
#

# ====== [ I. 1. Creat .LIBRARY_PARAMS.txt ] =====
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/220204_NS500487_0027_AHFCJLAFX3_min3ReadByGrp.LIBRARY_PARAMS.txt ]

# ====== [ 2. Fusion file ] =====
#File_Name_Fusion	nb_found[4]
10-N3-12cycles-IDT.unmapped.bam	4
7-N3-12cycles-IDT.unmapped.bam	4
8-N3-12cycles-IDT.unmapped.bam	4
9-N3-12cycles-IDT.unmapped.bam	4
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//> ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//MS_profile_analysis_inputSeqVersion.sh ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//CATGTAGTC ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//TCTCT ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//A ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//A15 ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//> ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//MS_profile_analysis_inputSeqVersion.sh ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//CATGTAGTC ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//TCTCT ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//A ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//A15 ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//> ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//MS_profile_analysis_inputSeqVersion.sh ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//GTGATAGTC ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//TCTCT ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//A ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//A20 ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//> ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//MS_profile_analysis_inputSeqVersion.sh ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//GTGATAGTC ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//TCTCT ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//A ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//A20 ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//> ]
# module load samtools
# module load picard/2.8.2
# module load bwa/0.7.17
# module load java fgbio
# ========= [INFO] ==========
# Path In : /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output
# Type In : .unmapped.bam
# MS Info : /env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Ref/tabMSInfo.9MS.txt
# minReadByGrp: 3
# Rep Fusion : /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/
# Rep Profil : /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/4_MSprofil_min3ReadByGrp/
# List fusion: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3-5_BAM_Fusion_min3ReadByGrp.log
# minLen : 
# =============================
#

# ====== [ I. 1. Creat .LIBRARY_PARAMS.txt ] =====
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/220204_NS500487_0027_AHFCJLAFX3_min3ReadByGrp.LIBRARY_PARAMS.txt ]

# ====== [ 2. Fusion file ] =====
#File_Name_Fusion	nb_found[4]
10-N3-12cycles-IDT.unmapped.bam	4
7-N3-12cycles-IDT.unmapped.bam	4
8-N3-12cycles-IDT.unmapped.bam	4
9-N3-12cycles-IDT.unmapped.bam	4
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//------- ]
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# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//TATGG ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//AC ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//AC25 ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//> ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//MS_profile_analysis_inputSeqVersion.sh ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//AGTCGTG ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//CGTGG ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//AT ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//AT15 ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//> ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//MS_profile_analysis_inputSeqVersion.sh ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//AGTCGTG ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//CGTGG ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//AT ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//AT15 ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//> ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//MS_profile_analysis_inputSeqVersion.sh ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//TCAGGTG ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//CGTGG ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//AT ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//AT20 ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//> ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//MS_profile_analysis_inputSeqVersion.sh ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//TCAGGTG ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//CGTGG ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//AT ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//AT20 ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//> ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//MS_profile_analysis_inputSeqVersion.sh ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//GTCAGTG ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//CGTGG ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//AT ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//AT25 ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//> ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//MS_profile_analysis_inputSeqVersion.sh ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//GTCAGTG ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//CGTGG ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//AT ]
# [Creat: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp//AT25 ]
# ====== [ 3. Mapp Reads/BWA ] ====== 
# Wed Jul 3 11:48:42 CEST 2024
# Wed Jul 3 11:48:42 CEST 2024
# Wed Jul 3 11:48:43 CEST 2024
# Wed Jul 3 11:48:43 CEST 2024
# ====== [ II. Call Consensus Reads ] === < 1.Group Reads By Umi >
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 11:59:15 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:01:39 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:03:59 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:13:33 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:19:26 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:21:32 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:32:32 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:41:15 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:47:26 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:47:50 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:48:06 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:48:24 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:48:47 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:49:06 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:49:23 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:49:47 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:50:07 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:50:27 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:50:46 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:51:00 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:51:16 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:51:34 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:51:50 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:52:04 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:52:22 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:52:40 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:52:58 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:54:34 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:55:03 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:55:31 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:56:58 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:57:45 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:58:05 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 12:59:52 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 13:01:08 CEST 2024
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam --strategy=adjacency  --min-map-q=10  --edits=1 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar GroupReadsByUmi --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.merged.withUMI.bam --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam --strategy=identity  --min-map-q=10  --edits=0 --raw-tag=RX 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam ]
 -------

# Wed Jul 3 13:02:02 CEST 2024
# ====== [ Call Consensus Reads ] === < 2. Call Molecular Consensus Reads >
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/8-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/9-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3 --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.merged.withUMI.group.adjacency.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ]
# > java -jar /env/gfs/apps/fgbio/2.0.2/fgbio.jar  CallMolecularConsensusReads  --min-reads=3  --min-input-base-quality=10  --input=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.merged.withUMI.group.identity.bam   --output=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.bam ]
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ]
# Wed Jul 3 13:14:39 CEST 2024
# ====== [ Call Consensus Reads ] === < 3. profils analysis >
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq CATGTAGTC TCTCT A A15
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq CATGTAGTC TCTCT A A15
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTGATAGTC TCTCT A A20
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTGATAGTC TCTCT A A20
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GACTTAGTC TCTCT A A25
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GACTTAGTC TCTCT A A25
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTATGTG TATGG AC AC15
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTATGTG TATGG AC AC15
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq CTCGGTG TATGG AC AC20
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq CTCGGTG TATGG AC AC20
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ACAGGTG TATGG AC AC25
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ACAGGTG TATGG AC AC25
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq AGTCGTG CGTGG AT AT15
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq AGTCGTG CGTGG AT AT15
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq TCAGGTG CGTGG AT AT20
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq TCAGGTG CGTGG AT AT20
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTCAGTG CGTGG AT AT25
> MS_profile_analysis_inputSeqVersion.sh 7-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTCAGTG CGTGG AT AT25
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq CATGTAGTC TCTCT A A15
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq CATGTAGTC TCTCT A A15
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTGATAGTC TCTCT A A20
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTGATAGTC TCTCT A A20
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GACTTAGTC TCTCT A A25
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GACTTAGTC TCTCT A A25
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTATGTG TATGG AC AC15
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTATGTG TATGG AC AC15
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq CTCGGTG TATGG AC AC20
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq CTCGGTG TATGG AC AC20
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ACAGGTG TATGG AC AC25
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ACAGGTG TATGG AC AC25
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq AGTCGTG CGTGG AT AT15
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq AGTCGTG CGTGG AT AT15
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq TCAGGTG CGTGG AT AT20
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq TCAGGTG CGTGG AT AT20
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTCAGTG CGTGG AT AT25
> MS_profile_analysis_inputSeqVersion.sh 8-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTCAGTG CGTGG AT AT25
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq CATGTAGTC TCTCT A A15
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq CATGTAGTC TCTCT A A15
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTGATAGTC TCTCT A A20
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTGATAGTC TCTCT A A20
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GACTTAGTC TCTCT A A25
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GACTTAGTC TCTCT A A25
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTATGTG TATGG AC AC15
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTATGTG TATGG AC AC15
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq CTCGGTG TATGG AC AC20
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq CTCGGTG TATGG AC AC20
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ACAGGTG TATGG AC AC25
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ACAGGTG TATGG AC AC25
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq AGTCGTG CGTGG AT AT15
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq AGTCGTG CGTGG AT AT15
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq TCAGGTG CGTGG AT AT20
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq TCAGGTG CGTGG AT AT20
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTCAGTG CGTGG AT AT25
> MS_profile_analysis_inputSeqVersion.sh 9-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTCAGTG CGTGG AT AT25
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq CATGTAGTC TCTCT A A15
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.A15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq CATGTAGTC TCTCT A A15
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTGATAGTC TCTCT A A20
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.A20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTGATAGTC TCTCT A A20
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GACTTAGTC TCTCT A A25
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.A25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GACTTAGTC TCTCT A A25
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTATGTG TATGG AC AC15
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AC15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTATGTG TATGG AC AC15
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq CTCGGTG TATGG AC AC20
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AC20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq CTCGGTG TATGG AC AC20
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq ACAGGTG TATGG AC AC25
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AC25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq ACAGGTG TATGG AC AC25
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq AGTCGTG CGTGG AT AT15
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AT15.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq AGTCGTG CGTGG AT AT15
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq TCAGGTG CGTGG AT AT20
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AT20.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq TCAGGTG CGTGG AT AT20
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.adjacency.consensusUnmapp.seq GTCAGTG CGTGG AT AT25
> MS_profile_analysis_inputSeqVersion.sh 10-N3-12cycles-IDT.AT25.min3ReadByGrp.merged.withUMI.group.identity.consensusUnmapp.seq GTCAGTG CGTGG AT AT25
# ========[ END ]========
# Wed Jul 3 13:20:11 CEST 2024
